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- PDB-5zqr: Tankyrase-2 in complex with compound 40c -

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Basic information

Entry
Database: PDB / ID: 5zqr
TitleTankyrase-2 in complex with compound 40c
Components(Tankyrase-2) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Tankyrase / PARP / ADP-ribosylation / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / protein polyubiquitination / Regulation of PTEN stability and activity / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. ...YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-9H9 / PHOSPHATE ION / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNiwa, H. / Shirai, F. / Sato, S. / Yoshimoto, N. / Tsumura, T. / Okue, M. / Shirouzu, M. / Seimiya, H. / Umehara, T.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
Authors: Shirai, F. / Tsumura, T. / Yashiroda, Y. / Yuki, H. / Niwa, H. / Sato, S. / Chikada, T. / Koda, Y. / Washizuka, K. / Yoshimoto, N. / Abe, M. / Onuki, T. / Mazaki, Y. / Hirama, C. / Fukami, T. ...Authors: Shirai, F. / Tsumura, T. / Yashiroda, Y. / Yuki, H. / Niwa, H. / Sato, S. / Chikada, T. / Koda, Y. / Washizuka, K. / Yoshimoto, N. / Abe, M. / Onuki, T. / Mazaki, Y. / Hirama, C. / Fukami, T. / Watanabe, H. / Honma, T. / Umehara, T. / Shirouzu, M. / Okue, M. / Kano, Y. / Watanabe, T. / Kitamura, K. / Shitara, E. / Muramatsu, Y. / Yoshida, H. / Mizutani, A. / Seimiya, H. / Yoshida, M. / Koyama, H.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3688
Polymers24,5152
Non-polymers8536
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-43 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.728, 66.728, 115.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1324-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Tankyrase-2 / / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 19150.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pCR2.1TOPO / Production host: Cell-free synthesis (others) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide Tankyrase-2 / / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 5364.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pCR2.1TOPO / Production host: Cell-free synthesis (others) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 147 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn / References: NAD+ ADP-ribosyltransferase
#4: Chemical ChemComp-9H9 / 2-[4,6-difluoro-1-(2-hydroxyethyl)-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one


Mass: 416.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26F2N4O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 2.4M (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→47.18 Å / Num. obs: 26944 / % possible obs: 99.9 % / Redundancy: 11.9 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Rsym value: 0.067 / Net I/σ(I): 27.1
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1395 / CC1/2: 0.762 / Rpim(I) all: 0.33 / Rrim(I) all: 1.146 / Rsym value: 1.096 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQO

5zqo


Resolution: 1.75→36.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 17.67
RfactorNum. reflection% reflection
Rfree0.19 1362 5.09 %
Rwork0.163 --
obs0.165 26875 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 54 141 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081762
X-RAY DIFFRACTIONf_angle_d0.8552372
X-RAY DIFFRACTIONf_dihedral_angle_d15.5571027
X-RAY DIFFRACTIONf_chiral_restr0.055231
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7517-1.78540.28051240.28242550X-RAY DIFFRACTION97
1.7854-1.82180.30111400.26312641X-RAY DIFFRACTION100
1.8218-1.86140.28281220.23592679X-RAY DIFFRACTION100
1.8614-1.90470.24671610.21512617X-RAY DIFFRACTION100
1.9047-1.95240.21181490.20362601X-RAY DIFFRACTION100
1.9524-2.00520.2131340.1882669X-RAY DIFFRACTION100
2.0052-2.06420.21851640.18182594X-RAY DIFFRACTION100
2.0642-2.13080.20251520.16422617X-RAY DIFFRACTION100
2.1308-2.20690.23721460.16552636X-RAY DIFFRACTION100
2.2069-2.29530.18181510.15452651X-RAY DIFFRACTION100
2.2953-2.39970.19341530.15822606X-RAY DIFFRACTION100
2.3997-2.52620.17761510.1552615X-RAY DIFFRACTION100
2.5262-2.68440.22261440.16072641X-RAY DIFFRACTION100
2.6844-2.89160.16611580.15252636X-RAY DIFFRACTION100
2.8916-3.18250.18691170.15082641X-RAY DIFFRACTION100
3.1825-3.64260.16391200.13762656X-RAY DIFFRACTION100
3.6426-4.58790.16211360.13412635X-RAY DIFFRACTION100
4.5879-36.51170.16891200.17782666X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98771.41481.99654.05495.67587.93340.3043-0.19320.0387-0.0896-0.40970.7599-0.1897-1.14790.51720.20440.00440.00510.3675-0.02210.4419-19.8768-10.2992-20.3055
29.0966-3.7143.83684.4554-1.95223.4141-0.02630.476-0.0408-0.1438-0.0713-0.02880.04460.14280.08640.1392-0.03180.03270.1819-0.01740.1297-2.5473-20.5568-23.22
31.7843-1.7122-0.53265.90552.3581.77580.07370.08790.0176-0.0637-0.17410.5016-0.0568-0.2160.07910.1316-0.01380.0430.23410.01330.2673-14.0488-13.6263-18.596
42.50722.8037-1.69665.6063-0.4876.4670.2745-0.1150.94940.4732-0.08480.6383-1.0642-0.0862-0.19540.40810.00790.00560.195-0.00960.3792-5.43288.0147-17.8077
51.20290.33010.27143.8047-0.80561.5960.0385-0.21360.04010.3574-0.04920.0424-0.14680.06990.01070.1524-0.01860.0370.24340.00460.163-1.2513-11.698-13.1746
65.345-1.7246-0.21885.43030.23732.72930.0697-0.49010.29660.36140.0544-0.52330.02380.4789-0.09610.2387-0.0941-0.01460.3587-0.01180.251312.5912-0.5936-18.9331
73.2911.3641-0.64183.352-0.83621.4667-0.0189-0.0175-0.0790.0053-0.0063-0.1662-0.02520.0930.01870.12370.004-0.00190.18280.00580.08870.9576-11.329-19.254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 952 THROUGH 962 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 963 THROUGH 991 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 992 THROUGH 1002 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1003 THROUGH 1019 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1020 THROUGH 1102 )
6X-RAY DIFFRACTION6(CHAIN 'A' AND (RESID 1103 THROUGH 1113 )) OR (CHAIN 'B' AND (RESID 1116 THROUGH 1123 ))
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 1124 THROUGH 1161 )

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